1. It is not always possible to track trophic interactions between predators and prey by direct observation. This is especially true when observing small or elusive animals with cryptic food-web ecology. Gut and/or faecal analysis can sometimes allow prey remains to be identified visually but is only possible when a component of the diet is resistant to digestion. In some cases there are no solid remains, and when there are it can lead to bias in interpretation of prey choice. 2. Numerous invasive and non-invasive methods have been developed to characterize predator-prey interactions but two principal areas dominate 'molecular' research. These are reviewed under the headings of monoclonal antibodies and DNA-based techniques. 3. Early 'molecular' studies of predator-prey food webs were dominated by the development of monoclonal antibodies. These methods continue to be used for mass-screening of field-collected arthropods for insect-specific proteins. 4. The application of species-specific primer design, polymerase chain reaction (PCR), restriction fragment length polymorphism analysis (RFLP), DNA cloning and sequencing, comparative sequence analysis (e.g. BLAST; basic local alignment search tool), high-resolution gel electrophoresis, Temperature/denaturing gradient gel electrophoresis (TGGE/DGGE) and automated fragment analysis with fluorescent probes is reviewed. The development of molecular techniques for use in predator-prey studies is primarily limited by their cost and the development of new procedures and equipment that complement them.